There are two main objectives to this level, each with two parts. There are several non-contiguous areas linked by one-way teleporters, making the layout of this level one of the more interesting in the game. It doesn't matter what order you do the four parts in. Within the room where you begin are two storage rooms with sealed doors, and the end of a conveyor in a glassed-in area that, if you look inside, has a boxing machine and a teleporter sending the boxed items off somewhere. One of the storage rooms has a hole in the wall in the back; the one you can't get into has a teleporter.
Missile packing station[edit]
Take the door from the first room to the front biogen-tank room. The door to the left goes to the back biogen-tank room next to this room. You'll see two unpowered Mazrium platforms: look for and shoot the shootable switches by the door and on the left wall to power them and start them moving. Take the platforms to the far end of the room, where you'll find a vent high up on the wall. You'll also see another shootable switch next to the vent. There's something special about this shootable switch. (Insert smiley here.) Remember it; we'll get to it later.
Shoot the vent and follow the air duct to the storage room next door. (You could see in here from the broken door in the biogen-tank room.) As you exit the air duct, look to your left for a 2x2x3 stack of crates reaching to the ceiling. Activate it and it lowers, revealing a rather sneaky secret area. Snoop around in the room; there are several items among the crates. Across the room from the door is a small side room with a vent inside. Follow this air duct to the missile-packing room. Find and take the teleporter in here, which goes to a control room. You'll see the power switch up out of reach. Stand on the octagonal structure and the center rises up, allowing you to reach the switch and power down the missile conveyor.
Take the door, which goes to a big room with doors and walkways in the four directions, a column with teleporters up on it, and bio-muck channels below. The other three doors go to the other control areas, but they only open from the other side. If you're after taking out every enemy, jump down to the bio-muck and get rid of all the Gryklaan so they won't be shooting at you. But it's no big deal really, because you'll only be in this room a few seconds at a time. The teleporter on your side of the column goes to the back biogen-tank room. The teleporter to get out of the bio-muck goes back to the level entrance.
Munitions packing station[edit]
Go to the first room near the level entrance. There are two vents and air ducts leading from here; one is caved in but has a full-health inside. Follow the other duct to the munitions-packing room. There are items in that storage alcove behind the drop chute. Now, that door at the far end of the room ... it isn't really necessary unless you're after every secret area. In either case, put it aside for a minute. Take the teleporter in this room to the control room it goes to, and hit the switch to shut down the packing equipment. The teleporter on your side of the column outside goes to the front biogen-tank room.
Now, if you want to get inside that door, go back to the munitions-packing room. You've probably already guessed that the "special" shootable switch in the front biogen-tank room opens this door. Here's the hard part: you'll need to shoot missiles, using remote-guidance mode, through the tunnel in the wall where the conveyor goes, through the door in the first room and across the front biogen-tank room to the switch. With the machinery off there won't be stuff on the conveyor getting in the way. Also, the grating at the end of the conveyor won't get in the way. The first missile will impact the door, opening it. You'll need to shoot again while the door is open. To be honest, you'll probably end up using a whole lot of missiles on this. And all this for what? One solitary Death Sphere. Joy in the journey, you could say. (It seems sensible to try using a Controllable Hoverdrone (#13) because they're much easier to use, but for some reason they won't impact the switch.)
Front biogen tanks[edit]
Go to the front biogen-tank room, and take the teleporter off to the right near the broken door. This goes to a large room. Hit the switch in the small control booth in the middle of this room to drain the front biogen tanks. When you leave, watch out: those black cylinders on the ceiling were concealing gun turrets. They've retracted now and the turrets are active. Outside, the teleporter on your side of the column goes to the storage room next to the front biogen-tank room.
Back biogen tanks[edit]
Go to the back biogen-tank room, and take the Mazrium platform to the far end of the room (shoot the shootable switch near the door to activate it). Up on the wall to the left is a nook with a Geosurvey: a not-so-secret secret area. Take the teleporter to a room with a bunch of conduits and a control console up on a ledge. Hit the switch on the console to drain the back biogen tanks. The teleporter on your side of the column outside goes back to the first room.
Leaving the factory areas[edit]
After you've drained both sets of tanks and shut down both packing stations, all of your tasks in the factory areas of the Citadel are completed. All that's left is to find your way to the biolab areas. Go to the storage room next to the front biogen-tank room. There's a vent at the far end; the duct in here is the caved-in one you probably saw the other end of earlier. There's a teleporter in the duct; take this to a small room with another teleporter and two side rooms with items. Activate the back wall in the side room on the right for a secret area. Take the teleporter, which leads to the closed-off storage area in the first room. There are several items in here, including a Big Buddy on the three-high stack of boxes. Take the teleporter in here. Ahead is a long, dark passage with a conveyor going down it, and sludge down below on each side. There are many, many gun turrets along the way--this would be a good area to set off a Death Sphere. At the far end is a large area to catch your breath, and the level exit. (If you come here earlier, there will be a closed door here until you complete the objectives.) Back at the near end of the conveyor is a teleporter leading back to the level entrance, if you want to go and collect stuff. When you've finished, make your way to the exit and proceed to the biolab areas.